(I assume) is for the same reason most papers use that equation. Consider the firm's problem, that they want to maximize profit, which is (total) revenue ($p_t \times y_t$) minus costs (which we can consider as the total cost of labor, which is $w_t \times l_t$, and capital, which is the rental cost of capital times capital used, $r_t \times k_t$). Therefore, we're trying to maximize:

$$\max_{l_t,k_t, w_t, r_t} \{ p_t y_t - ( w_t l_t + r_t k_t ) \}$$

If we normalize price of the output to $1$, we can solve for the optimal prices of labor and capital by solving the above problem. Taking the inputs one at a time, we get the first order conditions for labor:

$$0 = \frac{\partial y_t}{\partial l_t} - w_t$$

Which, of course, rearranges to

$$w_t = \frac{\partial y_t}{\partial l_t} $$

and for capital:

$$0 = \frac{\partial y_t}{\partial k_t} - r_t$$

which rearranges to:

$$ r_t = \frac{\partial y_t}{\partial k_t} $$

Of course, these are pretty standard derrivations across different fields of economics, so their exact reasoning might be slightly different, but this methodology should provide some of the clearest insight into why that's the case.